determine_anchor_overlap: Identifies Overlapping Anchors
In idr2d: Irreproducible Discovery Rate for Genomic Interactions Data

Description Usage Arguments Value Examples

Identifies all overlapping anchor pairs (m:n mapping).

1	determine_anchor_overlap(rep1_anchor, rep2_anchor, max_gap = -1L)

rep1_anchor

data frame with the following columns:

column 1:	`chr`	character; genomic location of anchor in replicate 1 - chromosome (e.g., `"chr3"`)
column 2:	`start`	integer; genomic location of anchor in replicate 1 - start coordinate
column 3:	`end`	integer; genomic location of anchor in replicate 1 - end coordinate

rep2_anchor

data frame with the following columns:

column 1:	`chr`	character; genomic location of anchor in replicate 2 - chromosome (e.g., `"chr3"`)
column 2:	`start`	integer; genomic location of anchor in replicate 2 - start coordinate
column 3:	`end`	integer; genomic location of anchor in replicate 2 - end coordinate

max_gap

integer; maximum gap in nucleotides allowed between two anchors for them to be considered as overlapping (defaults to -1, i.e., overlapping anchors)

A data frame containing overlapping anchor pairs with the following columns:

column 1:	`rep1_idx`	anchor index in data frame `rep1_anchor`
column 2:	`rep2_idx`	anchor index in data frame `rep2_anchor`

rep1_df <- idr2d:::chiapet$rep1_df
rep2_df <- idr2d:::chiapet$rep2_df

rep1_anchor_a <- data.frame(chr = rep1_df[, 1],
                            start = rep1_df[, 2],
                            end = rep1_df[, 3])
rep2_anchor_a <- data.frame(chr = rep2_df[, 1],
                            start = rep2_df[, 2],
                            end = rep2_df[, 3])

anchor_a_overlap <- determine_anchor_overlap(rep1_anchor_a, rep2_anchor_a)